Stargate Atlantis: S7 The Fossil Key Part Four Trophic Cascade
by the morrighan
Summary: These stories are a continuation from the season 6 stories to be found in the T sectin. This is the fourth story in the series of five. The city of Atlantis is ready to rise from the waves but the enemy still looms.
1. Chapter 1

Stargate Atlantis: S7 The Fossil Key

Part Four: Trophic Cascade

Jason Reynolds was nervous.

He was moving through the control room, eyes on the monitors. Power was flaring wildly. Atlantis was inexplicably coming alive and the whole city was stirring from its enforced slumber. It had been submerged in the ocean depths for almost a month, and it appeared that it had decided that it was time to awaken. There was nothing Jason could do about it. Try as he might he was locked out of every system. He swore, trying different keyboards but they were unresponsive. "Are the comms up yet?"

"Not yet!" Amelia Banks-Dex was typing furiously at a computer, trying to access the city as well. "Everything but the…wait!" She tapped her earpiece. "Colonel Sheppard, report! Doctor McKay, please respond! We have a massive power surge and are locked out of the controls!" she shouted into the PA unit. Static squealed in response. "Damn it! It's like she's shutting us out!"

"She?" Jason asked with a quick smile.

Amelia shrugged. "Guess that terminology is catching," she quipped. Often both Colonel Sheppard and Doctor Beckett would refer to the city as she; more specifically when they were connected to the AI's interface. "I can't even access the secondary systems!"

"Well, someone is," Jason remarked. He glanced across the room and down to the inert Stargate. He looked beyond that to see through the windows. The shield holding back the ocean's pressure was a pink sheen all around them.

There was a faint rumbling and the city moved. The walls shook and the shield that was holding back the ocean waters shimmered. Atlantis was ready to rise once more, whether or not the humans inhabiting it agreed.

"Can you shut that off?" Ronon Dex asked. He caught a console as the floor canted to the right. There was an audible hum in the air. He could feel the static charge of electricity as the city was in the midst of a reboot. The hairs on his arms stood up and he freed the console. Although he did not have the ATA gene the power appeared to be increasing.

"No! Every system is unresponsive!"

"We have a bigger problem! Look!" Jason pointed at a screen. The monitor was scanning the two alien ships that had been in orbit for a month. The two blips were moving across the sky; above the planet but perilously close to breaking atmosphere and descending. "They're heading for the open ocean!"

"They're heading for us!" Amelia realized. "They must be reading our power surges! Damn it! If we can't get this shut down they will find us and there's no way we can stand against them!"

"Why aren't Sheppard or McKay responding?" Jason asked worriedly. He tapped his earpiece. It filled his ear with static.

"I'll go." Ronon moved to the door and forced it open with brute strength.

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Rodney McKay was worried.

He paused in the doorway to the Chair room, stunned by the scene of utter destruction. The second Chair had exploded, and it appeared that most of the blast had been contained in this one room. He had had to open a panel to override the lockdown and get the door open. Now he stood, surveying the sea of carnage that littered the floor and the walls.

In the midst of the destruction the Ancient Chair native to Atlantis stood, untouched. It was surrounded by a blue force field, protected from the violence. Upon the Chair sat John Sheppard, eyes closed, reclining and lost in the interface.

Lights flickered like tiny stars in the surrounding gloom.

"John!" Moira O'Meara shoved past Rodney and entered the room. She stepped past the debris and stood, staring at the military commander. He appeared to be asleep, but his body was tense, muscles straining. His hands were pressed to the controls on the arm pads. Sweat was beading his brow. A trickle of blood escaped his nose.

Rodney moved next to her. "Shit. We have to get him out of there now! Once I get the force field deactivated you need to get him out of the interface, Moira!"

"Okay. Okay, I can do that." She moved closer, clasping her cut wrist. The towel encircling it was turning red with blood. It stained her fingers.

"Okay. The second that force field drops—"

"I know! Do it already!"

Rodney smiled and darted to a wall panel. He moved to his knees and opened his lap top. "I'll need to cut the power here…end the connection…ah! These crystals!" He frowned, pulling crystals and wires and swearing as he worked, trying to sever the power connection. He began to pry up a floorboard, and grabbed a set of cutting tools.

Moira waited, waited, feeling dizzy but focusing on John. John needed her and she wouldn't fail him. "John? John, can you hear me? You need to drop the force field! John!" She stepped as close as she could, staring at him. Electricity buzzed the air like angry bees and lifted strands of her hair to waver weirdly. The floor tilted and she almost fell, catching herself. "Rodney, what's happening?"

"I don't know! He's accessing all of the power…or the city is. Crap." He inserted the tool and cut the wires. The snap was loud and a sudden spark made him reel backwards. Rodney glanced up as the lights flared, abruptly illuminating the room. "Go!"

"What? Oh!" The force field dissipated. Moira rushed to John. She touched his arm. She shook him. "John? John, wake up! You did it! You need to wake up now! John!" She shook his arm more forcefully, trying to remember how she had awoken him the last time. She leaned close to speak softly into his ear. "Naughty colonel. John?" She sighed, considering. "Violet. Push-up, plunging with lace. Thong, barely there, and sheer." She looked over to see Rodney staring at her, as she was describing her underwear. "What? It worked the last time!" She blushed.

"Did I say anything?" the physicist said, but he smirked and moved to the Chair after a cursory glance along her body.

"Damn it, John, come on!" Moira shook his arm again. She leaned closer, running her mouth up his neck to nibble his ear. He was oddly cold, despite the warmth of the room and the sweat beading along his neck. She considered again, frowning.

"Moira, we have to get him out of there now! Power levels are rising and if the fuglies detect them we will be in serious trouble! I can't access the mainframe!" Rodney warned, typing on his data pad. He frowned in frustration.

"Homo erectus and let me think!" she snapped. She clutched her wrist to her, leaning on the Chair and inadvertently providing more power as it responded to her ATA gene.

"If your underwear didn't do it for him what will?" he quipped.

"It's not funny and I…" She broke off, realizing. She leaned close again, speaking softly into his ear. "John? Yes. The answer is yes. Yes."

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John Sheppard woke. It was almost like a bubble popping. One second he was lost in the interface with the two AIs becoming one and the city exploding around him; the next he was in the Ancient Chair and Moira was whispering the answer he had wanted to hear to his marriage proposal, at long last. He opened his eyes, a smile on his handsome face. "About time, baby. You really shouldn't keep a guy waiting like…" His words fell away.

Moira was on the floor. Rodney was kneeling next to her, clasping her wrist where a towel was dripping crimson. Red dots lined the floor next to her.

John's heart skipped a beat. "Is she…" He powered down and the Chair righted itself.

"John, thank God! I had no choice! She was the only one who could get you out of there!"

John's heart skipped a beat. "Is she…" The words stuck in his throat and he was frozen, unable to move as he feared the worst.

"What? No! Sorry! She's weak from blood loss! We have to get her to the infirmary!"

"Jesus, Rodney, you scared the shit outta me!" John scrambled off the Chair and moved to take Moira into his arms. "Moy?"

"Sheppard! McKay! We're losing control of the city and the fuglies are heading this way!" Ronon shouted, rushing into the room. He froze, seeing the tableau of the two men on the floor with an unconscious woman between them. He glanced at the destruction all around them.

Moira's eyes fluttered and she stared up at John. "John?" She struggled to sit and John supported her, keeping her close in his arms, against his chest.

"What did you do to yourself, baby?"

"Accident, I…"

"Never mind, I've got you now." He scowled, seeing the bloody towel. He encircled her wrist with his fingers, pressing firmly. A soft moan escaped her lips. "Sorry, Moira. You need to be in the infirmary and—"

"No! No, John, I won't go there!" Moira objected strongly, trying to move but she felt weak and dizzy and John's hold was strong, although gentle. She fell back against his chest. He was warm, solid and secure as the room seemed to spin around them.

"Okay, Moy, not the infirmary," he quietly agreed to soothe her. He looked up at his two friends. "Ronon, have Reynolds lock down the Jumper bays and any other extraneous areas. Rodney, I need you to get to the lab and the containment field. You should have full power there. Fire her up and get that Penning trap into it, and get the systems online to weaponize it."

"What? Are you crazy? We can't do that, John!"

"We don't have a choice, Rodney! We need a huge explosion so the fuglies think there is nothing here, and if we can take out one or two ships of theirs so much the better! Now get to that lab and get it ready!"

"No! I already told you we can't do that! Every simulation I have run ends in a catastrophic release of energy going beyond our solar system! What's more it will rupture the shield and effectively drown Atlantis with us in it!"

"I know that! I'll handle it! Now get to that lab!" John tapped his earpiece. "Beckett, I need you and a med kit to the Chair room now!"

"No! I'm fine!" Moira struggled but John's arms enclosed her securely.

"Don't you worry, Moira, I'm right here. Carson is himself again," he soothed, seeing the panic in her brown eyes.

"How are you going to handle it?" Rodney snapped, clearly dubious.

John met the angry physicist's gaze. "Once Moira's okay I am going to access this power and raise the city."


	2. Chapter 2

Stargate Atlantis: S7 The Fossil Key

Part Four: Trophic Cascade2

Carson Beckett was anxious.

He ran through the city, swinging his med kit at his side like a battering ram as he ducked past moving doors and tilted as the floor bumped beneath him. Lights were flashing and Atlantis resembled a living, breathing creature that he had to navigate to get to his patient.

He headed for the lower levels, quickly descending the stairs, not trusting the transporters. He reached the Chair room and paused, seeing the destruction of the second Chair. A momentary memory assailed him; of how he had accessed that Chair; how a beautiful woman with red hair and an Irish accent had beseeched his aid; how another had nearly destroyed him and had taken over his mind.

"Carson!" John called, seeing the doctor standing in the doorway. He gestured with one arm.

"John! What's happened?" Carson headed for him but was brought up short seeing his patient. A sudden rush of memory hit him, of what he had done to her and he recoiled in guilt and shock. He remembered putting the electrodes onto her temple; he remembered the electroshock treatment he used to try to cure her of her hallucinations. It was as if he was a spectator in his own body; that someone else was pulling his strings like a mad puppeteer to torture the biologist, all in the name of science and medicine. "Moira?"

"She's cut her wrist, badly," John informed, still holding Moira to him as they sat on the floor. He smiled for a moment as Moira's hand was sliding across his thigh, across his lap which was unexpected and pleasurable, until he realized her trajectory too late.

Moira grabbed his 9mm and lurched out of his arms to her feet. "No!" She held out the weapon with both hands, ignoring the pain in her wrist, ignoring the blood trickling down her arm as the towel dropped to the floor like a crimson exclamation point. "You won't touch me again!"

Carson froze, anguish on his face and sorrow in his blue eyes. He set down his med kit. "Och, Moira…what have I done? I'm sorry, so sorry, love! I wasn't myself, it wasn't me but that still doesn't excuse me, not at all! Please, love, let me help you."

"No!" The gun wavered in her hands as she clicked off the safety. She stumbled as her vision blurred for a moment. She didn't see the female mirage, just the doctor, but her heart was racing with the fractured memories of what had been done to her.

John slowly moved to his feet and gestured for Carson to step backwards. "Moy? It's all right, Moira, I'm here. Carson's here to help you, okay? I'm right here."

"No, John. Get in the Chair and raise the city before the Homo erectus find us!" she ordered. She moved, keeping the gun trained on Carson.

Carson held up his hands. "Let John tend that wrist, Moira, please. I won't touch you, all right? Everything he needs is in the kit." He pointed at the little black bag on the floor.

"Okay, that's a good idea, Carson. Moira, lower the gun. I will get the kit and—" John froze as she pivoted and pointed the gun at him.

"No! Get that fine ass of yours into the Chair and save the city! Rodney's risking his life to get that Penning trap ready so you damn well better be prepared to use it once you raise the city!"

John's lips were forming a smirk but he scowled instead. He didn't like having a gun pointed at him, particularly his own gun. "Okay, sweetheart. First let me wrap up your wrist, okay? Lower the gun now."

Moira shook her head. She regretted it as the room swam. She turned to point the gun at Carson again as he had taken a tentative step towards her. "No! You stay the hell away from me! All of you stay the hell away!" She swung the gun towards John again, towards Carson, towards anyone else who might be threatening her. She remembered being forcibly held down and she wouldn't let it happen again.

They were all against her and she couldn't trust anyone.

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Rodney was concentrating.

He was working quickly but carefully as he activated the systems in the lab. Full power had been restored, and the computers were all running normally. The containment field was a humming circle of light and sound. Within its confines sat the Penning trap. It was an impossibly small item taken from the doomed sister city of Atlantis. It had been stolen from the fuglies and they wanted it back; never mind that it had taken centuries to retrieve it.

Rodney was loath to give it up. The thing was a marvel of engineering and physics. It was the size of a paperweight and contained both matter and anti-matter creating a geonium atom. It was a false atom of charged particles, frozen in a homogeneous static magnetic field and a spatially inhomogeneous static electric field. It contained great power; enough to power the city indefinitely and thus render the necessity of ZPMs obsolete. Conversely it could be used as a weapon strong enough to puncture a hole in reality, if misused.

Unfortunately he had to utilize the trap for the latter option, minus the massive destruction, hopefully.

Power was surging. He scrambled back from the machine and hastened to the computers. He tapped his earpiece, watching the power levels rise and rise. "Sheppard, copy? It's booting up now! You need to raise the city or we're all going to drown! John, do you read? John!"

Silence. He moved towards the containment field, pausing as the hum of electricity made his hair stand on end. The little Penning trap was spinning, spinning now, trapped in its own vortex of power. Rodney ran back to the computers and began the complicated calculations necessary to direct that destructive power outwards and away from the city.

He had to set a trajectory towards the enemy ships and as far from Atlantis as possible. He worried about the repercussions; the force of the expanded energy would travel for light years and possibly obliterate everything in its path, including planets. The harnessing of such energy was a delicate thing and Rodney knew only too well the consequences of such power.

He didn't want to destroy yet another planet or two.

He tapped his earpiece. "Sheppard? Sheppard, copy? You need to raise the city now or this thing will blow a hole in the shield! I can't stop it once the program is initiated! I am aiming it through the central tower core as that is the most protected but that shield needs to be down and for that to happen we need to be out of the water! John!"

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Ronon was curious.

He watched the monitors as the blips were getting closer to the ocean. He watched the power levels rising from the green to the red. Several alarms were sounding and the city was shaking like a dog after a long nap. He moved to stand next to his wife as she uselessly attempted to cut off the systems. "Sheppard knows what he's doing."

"Does he?" she snapped. "If we can't get this under control the fuglies will find us and kill us!"

"He's going to raise the city and obliterate them, or make it seem like we were obliterated," Ronon explained. His faith in his friend was unshakeable, even now.

"A subterfuge," he realized. "But how? If we fire the Drones that's a dead give-away and once we surface the shield will drop and we'll be vulnerable until we can activate the cloak," Jason mused.

"They might even see us with the cloak! They were able to detect a cloaked Jumper!" Amelia reminded. She brushed a stray stand of auburn hair that had escaped her bun off her face. "If he's not careful we could burn out a ZPM and then we would be dead in the water!"

"He knows what he's doing," Ronon assured. He eyed the screen. The two blips representing the two enemy ships were moving slowly, inexorably closer to where Atlantis was hiding in the ocean. So far no fighters had emerged from either ship and that was a good thing.

Nevertheless his fingers stroked the butt of his gun, just in case. He glanced at the inert Stargate. There was no power there so nothing could get through, and according to Sheppard the fuglies had no knowledge of the Stargate system.

Jason glanced at the Satedan. "Colonel Sheppard, what are your orders? Sir?" He tapped his earpiece but it was working fine now. He was just being ignored. "Doctor McKay, please respond. Colonel Sheppard, what are your orders?" he repeated. "Ronon, are you sure that he's in control?"

"Yes. He was out of the Chair and Rodney was with him."

"Wait, he was out of the Chair?" Amelia asked, startled. "Then who's flying the city?"

"I guess Atlantis is," Jason surmised with a shrug.

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"Moira. We don't have time for this," John said, round the noise of Rodney shouting in his ear. He stepped so he was in front of Carson. "Lower the weapon and hand it to me, please. Then I will get in the Chair and you can wrap up your wrist."

"John? John, are you real?" Moira felt light-headed and her vision was swimming. Her finger slid on the trigger as she stared at John, at Carson, at the destruction of the room. She glanced quickly at the shadows but there were no Homo erectus lurking and that was a good thing. She looked at John and Carson again.

Her head was thudding and her hands were slick with sweat. She felt light-headed and the floor tilted under her feet. She wasn't sure it if was the city moving or her own dizziness creating the effect. She only knew she wouldn't let anyone hurt her again and no one would hold her down on that bed while it was being done.

"Yes, I am real, Moy. You don't want to shoot me, do you? Lower the weapon or I can't raise the city. If I can't raise the city we will all drown. Moira?" He took a step towards her.

"Listen to him, love, please," Carson urged, taking a step towards his medical kit. He could see how pale she was. She had lost a lot of blood and was becoming disorientated.

"No!" She took a step backwards and stumbled. Her finger pressed the trigger.

The gun went off.


	3. Chapter 3

Stargate Atlantis: S7 The Fossil Key

Part Four: Trophic Cascade3

The city tilted.

Atlantis was rising and humming with power. The walls were singing as each section became activated and alive, each joining in harmony with the others and welcomed from the enforced slumber like a long-lost relative. The shield was a pink veil enclosing the city in safety, but it fluctuated, anxious to be free and out of the waters. Atlantis wanted to rise but lacked only one thing.

A pilot.

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The city tilted.

It saved John's life, as he lost his balance and swerved sideways. The bullet missed him, zipping past him and grazing Carson's arm as the doctor had the misfortune to fall the other way, almost in the path of the bullet.

John scrambled to retain his footing. He lurched towards Moira as she fell. The gun dropped from her sweaty grasp and skittered towards the Ancient Chair. John caught her before she slammed headfirst into the device. He gently set her onto the floor. "Carson! Take care of her now!" He leapt up and threw himself into the Chair.

The Chair reclined as the power filled it. John touched the controls, activating them. He took a moment to watch as Carson scurried to Moira and began to tend her cut wrist. John relaxed into the interface and it felt right, it felt like it should and seemed to be even stronger. He eyed the star chart dancing in the air above him and saw the position of the two fugly ships in orbit above the planet. They were approaching the ocean where Atlantis lay and one was beginning to descend into the atmosphere.

"Citywide," John ordered and he heard an answering click in his earpiece. "Listen up, people! I'm in control now! Don't touch any of the systems until I give the word! Rodney, when that Penning trap reaches full power in the containment field you let me know. Atlantis is rising and we are going to eliminate this threat! Sheppard out!"

He cut off the clamor and looked at Moira. She was still on the floor, unconscious. "Carson?"

The doctor glanced at him. "She'll be fine. She needs fluids. I need to move her to the—"

"Negative. Bring the IV here. She doesn't leave my sight." He glanced at the bandage on her wrist, at her pale face, at the bruises on her temple.

"John! I can't treat her properly here! I need to—"

"No, doc. You treat her right here. She doesn't leave my side, got it? Go!"

John waited until the doctor acquiesced and hastened to gather what he needed. John closed his eyes and concentrated, flexing his hands over the controls. "All right, baby, here we go. Up and out and let's blow them to kingdom come…and give the rest a fucking message they can't ignore. Here we go now."

The city seemed to purr in response.

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Amelia almost jumped when Colonel Sheppard's voice sounded over the PA, loud and clear and giving orders. She felt a wave of relief, then irritancy. "Colonel? You're going to raise the city? The fuglies are almost above us now! Colonel!"

"Standby on all systems," Jason Reynolds said, stepping back from the consoles. He grabbed a chair as the floor tilted again and the city seemed to shake, eager to be off the ocean floor. He glanced at the walls and the water bubbling there seemed to be flowing upwards, not downwards, as if it would defy gravity.

"Told you," Ronon Dex said with a grin. He shared his confidence with Jason but his wife was still frowning. "What?"

"What? Are we even going to make it? The systems are haywire! I have no control at all! Where the hell is McKay?" she snapped. Her fingers flew over a keyboard but nothing was happening, nothing at all. She was tempted to slam her fist onto the machine.

"He's in the lab getting that trap ready," Jason answered. "This is gonna be real close."

"Too close! Has Sheppard lost his mind!" Amelia fumed.

"He knows what he's doing," Ronon assured, eying his wife now. Her vehement objections were out of character and he wondered about it.

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The city tilted.

Rodney was knocked backwards but he stubbornly clung to the console. "Sheppard…power's reaching maximum level output, copy?" He moved to the keyboard and tapped the command codes. He raised his eyes to the containment field. A force field shimmered, protecting the physicist as the circular enclosure lit up and vibrated with power.

The Penning trap within was spinning like a top. The power rush was audible, like a hornet buzzing in Rodney's ear. He glanced around as the city shook and he could feel the star drives being accessed. The floor was vibrating under his feet and the walls were shaking. It was almost like an earthquake.

"Sheppard! Levels are rising…we're almost there. If we're not out of the ocean and if that shield isn't down we'll be—"

"Acknowledged, McKay! On my mark issue the final command!"

"Acknowledged!" Rodney's finger hovered over the button as he kept one eye on the brightly lit, humming containment field and the other on the rising power levels. "Better make it fast!"

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Moira stirred and moaned. She felt like she was sliding on the floor and she sat, disorientated. The floor was titling under her. She stared at her wrist where a bandage encircled her cut. She stared at her other wrist, seeing the bruise. She stared at her hand, eying the mysterious gold ring on her fourth finger.

Finally she turned and stared at the Chair. John was sitting there, reclining and relaxing into the interface of man and machine. His handsome face was calm, composed and serious as his brows furrowed. His long fingers flexed on the control pads. Moira scooted closer, not trusting her legs as they felt wobbly. "John?"

John was concentrating but he paused, hearing Moira's voice. She wasn't in distress so he relaxed. "Easy, baby."

"Are you talking to me or to the city?"

He chuckled. "Both. Are you okay, Moy?"

"Yes. Oh, sorry! I shouldn't break your concentration."

"It's all right. Stay here with me." He opened his eyes to see her staring up at him. He nodded, gauging her condition to be better. He closed his eyes again. "Here we go, baby. Moira, stay close to the Chair."

"Okay, John. John, are you okay? I…I seem to remember…a gun…a…"

"I'm fine, sweetheart. We'll talk later, once I get this taken care of."

"But the gun…" She stared at the 9mm handgun on the floor near the Chair. Her memories were foggy but she could recall holding it and pointing it and shooting it. She sighed, uncertain. She shakily moved to her feet, wincing at the pain in her ankles and wrists and head. She stepped to the Chair and touched it, touched John's arm. "John…John…are you real?"

"Yes, Moira," he assured, keeping his eyes closed as he felt her fingers on his arm. "Hold on, sweetheart, here we go."

"John? I can't…I can't quite remember…everything but I remember some things…they…" She stumbled and leaned on the Chair. The power increased and seemed to sing under her.

"Okay, honey. Stay right here with me and help me fly the city. I could use your mojo."

"I bet that's not all you could use," she commented, glancing down his body to see his pants tenting.

He snorted with amusement. "Later, baby, you got that right."


	4. Chapter 4

Stargate Atlantis: S7 The Fossil Key

Part Four: Trophic Cascade4

The city rose.

Atlantis lifted off the ocean floor, shaking off the sediment and grit like a lady demurely shaking out her skirt. Water plumed all around and the displacement sent waves crashing in every direction. The shield hummed. It was a pink gem rising through the blue-green waters, heading for the surface as surely as a flower turns its head towards the sun.

The surface was beckoning. Atlantis had been asleep for too long and she was ready to reclaim her rightful place in the galaxy. All of her parts were whole and joined and filled with power. Her able pilot was guiding her effortlessly as the mind and machine connection was almost seamless now.

The star drives purred under his touch, responding to his commands which rendered the controls all but useless. His fingers glided over the arm pads but it was his mind that was really directing the spaceship now to rise and ready itself for battle.

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The city rose.

John reclined in the Ancient Chair, tense but otherwise at ease. He was in complete control. The city was bending to all of his wishes; obeying his every command and it was almost a turn-on, if it had been a woman. He smirked at the thought. His fingers glided over the controls but it was his mind that was directing the ship now. His ATA was bonding with the city's interface and together they would raise the city and take on the fuglies.

Only if necessary. John had a plan and was determined to see it through, convinced it would work. He felt Moira's grasp on his arm and it centered him, calmed him. She trusted him to do the right thing; to get them to safety and he vowed that he would. He would protect her at any cost, at all costs.

John licked his lips. "Rodney, on my mark initiate your program. I'm going to send a counter-measure to limit the blast radius so don't worry. Copy? ETA is three minutes." He opened his eyes to see Moira watching him, worry on her pale face. Her brown eyes were huge, pupils enlarged despite the lights in the room. "Sweetheart? Are you sure you're okay?"

She blinked. "John? Yes."

He frowned. He reached over and touched her cheek. "We'll get some food and then into bed soon, I promise. Relax, Moy. No one is going to hurt you ever again."

"Shouldn't you be flying the city?"

"Huh? Oh, yeah." He smiled at her expression and closed his eyes. "Here we go, baby. Give yourself to me. Give me everything…I'll make you do every little thing for me, everything you want and were too timid to ask I'll make you do and you will beg for more."

"Um, John?" Moira asked. His voice was low, gruff and sent a sensual shiver along her skin. Her fingers moved along his arm. "You're talking to the city, right? John?"

He smiled in response.

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The city rose.

Rodney McKay watched in awe as the power levels rose and Atlantis came to life. He could feel the sheer magnitude of the star drives. Although primarily a city first and foremost Atlantis was a spaceship, and the engineering feat was astounding. Rodney could almost imagine hearing the water crashing around them as the city flew upwards, escaping the water.

He scowled as John's voice sounded in his ear. "Copy that! Three minutes? Is that an arbitrary number or an actual time? Never mind, I'll be ready!" He stared at the containment field, but had to shield his eyes as the lights were spinning now and too bright. In the middle was the Penning trap, spinning wildly and rising off the floor like a beacon.

Rodney checked the monitors. He swore. "John! It has to be now! We're approaching critical mass too quickly! John!"

"Negative, Rodney! We haven't cleared the ocean yet!"

"Too bad! If this goes critical it won't matter if we're clear or not! I'm initiating the sequence now!"

"No! Belay that! We need to clear the ocean first!"

"We can't wait, John! It's going critical now! Initiating sequence! You better have those counter measures ready now! Now!"

Rodney grabbed the console as the room shook. He squinted, turning away as the light was unbearable and a whining filled the air. With a pop the containment field shot the Penning trap upwards and out of the city.

He traced it with the computer, following its path through the city, up through the city's spire. It was moving impossibly fast, gaining more power as it sped along. In mere seconds it would smash through the tower and cut a hole in the shield, disrupting the interface and creating a power vacuum that would drown them all.

Rodney braced himself for the tremendous blast and imminent doom.

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The city rose.

Carson ignored the shaking walls and wailing alarms. He ran into the infirmary, mind racing over what he would need to help Moira. She needed fluids, possibly even plasma and he eyed the IV drip. It would be awkward dragging that through the city. A shot would be better. He moved to the medical cabinet but froze.

The bed was empty, but the restraints on them remained. They were lined with dried blood.

A shiver stole up Carson's back. He stared, shocked at the memory of what he had done. He had been trying to help Moira and eliminate whatever had been causing the hallucinations but instead something had taken over and he had tortured her. He had broken the Hippocratic Oath of do no harm and he wondered if his friendship with Moira had been irreparably broken as well.

A wave of emotion threatened. He forced it down, concentrating on what he could do now; not what he had done in the past. He glanced at the array of pills in the cabinet, knowing some of them would help calm him and control his horrified responses. But it wasn't time for that now. He needed to remain clear-headed. He looked away from the cabinet, deciding what to do.

Nevertheless his gaze remained locked on those bloody restraints.

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The city rose.

"Brace yourself!" Jason shouted. He grabbed onto a console in the control room, eying the screen as it displayed a graphic of Atlantis rising through the ocean towards the surface.

"How much time?" Amelia shouted, holding onto a table. She stared at another monitor displaying the enemy ships. They were closer now, almost over the ocean where Atlantis was rising. One ship had descended from orbit and was perilously close to the lower atmosphere. "They're in position! If they fire we are done for! Colonel Sheppard, do you read? They'll see us if we breech the surface!"

"What's that?" Ronon looked round as a rumbling superseded all over sounds, even the alarms that were pinging in unison. He hastened to the window to see the pink shield that was protecting them from the water begin to shimmer and shake like a snow globe. "The shield's failing!"

"What? Shit!" Jason ran to his side to see the odd effect. "Colonel Sheppard! The shield is failing and we are still under water! Doctor McKay, do you read? McKay?" Static buzzed in his ear and Jason swore. He ran to the monitors. "I'm detecting a massive power surge out of the lower levels and it's rising…it's rising through the city's tower!"

"McKay." Ronon left without another word.

Jason tapped his earpiece. "Colonel Sheppard, do you read? We are approaching ZPM overload! Colonel!" Jason shook his head, out of his element now as everything was happening at once and he had no control over anything.

"Fuck this! I'll get him out of that damn Chair!" Amelia rose and ran out of the control room.


	5. Chapter 5

Stargate Atlantis: S7 The Fossil Key

Part Four: Trophic Cascade5

The shield collapsed.

The pink shimmer dissolved, dropping like a sequined curtain. Luckily Atlantis had just emerged from the ocean waters and hovered above the massive displacement of waves that plumed in all directions. The beaches of the mainland would be inundated by the tsunami-force of the water.

At the same time the Penning trap streaked out of the city and directly up into space.

At the same time two Drones were fired and flew with unerring accuracy not towards the Penning trap but towards each other. The missiles collided and the resultant explosion propelled the Penning trap as it imploded into an enemy ship. The two catastrophic events contained each other and cancelled each other out, but not before the one fugly ship had been blown to pieces.

Before the fallout could harm Atlantis the shield rose again and the city settled on the surface of the ocean, rocking gently in the currents. The hailstorm of debris and detritus and radiation fell harmlessly around the city and created violet sparks on the shielding.

Atlantis was safe.

Atlantis was whole.

Atlantis was home.

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Rodney started in shock at the monitors. His fingers flew over the keyboard but the results were the same. Two massive explosions had occurred above the city, above the ocean and in the atmosphere. He glanced at the containment field. The machine was dark, powered down now that it was empty.

"McKay!" Ronon ran into the room, halted. "Are you okay?"

Rodney glanced at the Satedan. "Of course. He…he did it! I don't know how but he did it! Wait! I do know how!" The physicist eyed his computer screen. "The Drones..of course! They utilize a different type of energy which would effectively negate the magnetic and electrical fields once the atoms smashed! How the hell did John know that?" he mused. "More importantly how did he realize that ahead of me?"

Ronon grinned. "I don't know, but he did. What about the fuglies?"

"Huh? Oh…I don't know. We need to get to the control room! I need to adjust the power levels and the ZPM output for the shield. I think we're in the free and clear, at least for now." He tapped his earpiece. "Sheppard, copy? Oh shit! We need to get the city's ballasts set or we will be free floating!"

"We need to see if the fuglies are still there," Ronon added as the two men exited the lab.

"We need to eat! I haven't had food in hours!" Rodney exclaimed.

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Amelia ran through the lower levels. It was easy to run since the city was stabilized now but the threats still loomed. She flew down the stairs and the hallways, and rushed into the room where the Ancient Chair resided. "Colonel! You have to stop this right now!"

Moira whirled at the interruption. She stared at the other woman. She quickly snatched the 9mm handgun off the floor and pointed it at the major, adopting a shooting stance as she held the weapon with both hands. "Stop right there!"

Amelia froze, startled. She glanced past Moira to see John reclining in the Chair. His handsome face was a study in concentration as he moved slightly, guiding the city. "He needs to stop this now before the fuglies find us!"

"No. He is taking care of the problem. If you interrupt him now the city won't make it."

"He has to stop!"

Moira clicked off the safety. "I said no! I know what you did. I remember! I remember what you all did! You held me down. You held me down while that thing in Carson tried to fry my brain!"

"What? No! Carson and I were trying to cure you!" Amelia countered.

"Stay back or I'll shoot!" For emphasis Moira pointed the gun at the floor and shot. The bullet pinged along the floor, making Amelia jump and grab her own weapon.

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Jason hit a few buttons. The display revealed a jumble of readings, indecipherable but the two blips were gone. One was completely gone and the other was heading away from the planet. He looked up as Rodney and Ronon ran into the control room. "Thank God! I can't get the cloak to initiate and the—"

"Move!" Rodney shoved the hapless major aside and accessed the system. "We won't cloak while the shield is up and the shield won't come down until it deems it safe. Automated systems are coming back online." He moved to another monitor. "I've got to reroute this ZPM output. The city's locking down the ballasts…must be an automated system to keep us tethered in one place…unless…John? John, do you read me? And we've got to repair that hole in the spire…except it's already been repaired…what the hell? John?"

"What about the fuglies?" Ronon asked, moving to eye the other screen.

Jason pointed. "One ship's been blown away. The other is limping away from us."

Ronon grinned.

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John relaxed into the interface and slowly let go, releasing control to the automated systems. He opened his eyes and stared. Two women were standing near the Chair, each pointing a gun at the other, and while the scenario was a hot one the sound of Rodney shouting in his ear ruined the mood. He let his gaze rest on Moira for a moment, at her stance of legs apart and arms raised. He eyed her shapely rear a moment before he moved and the Chair righted itself. Power quietly decreased. "Moy?" he asked.

Moira didn't move. "It's all right, John. I've got your back."

"She's crazy, sir! You have to stop now before you get us all killed!"

"Rodney, copy that. Reroute the ZPM output and let the city do the rest. Yes, it will!" he said over the physicist's ranting. "Get Reynolds to track that other fugly ship! As soon as we are clear we will cloak but I want that ship tracked! Sheppard out. Major, stand down!"

"Sir, with all due respect I—"

"I just gave you an order, major!"

Amelia sighed and slowly lowered her gun.

John glared. He got out of the Chair and stepped to Moira's side. He touched her arm. "Moira? Thanks. It's all right now. Moira?"

She glanced at him. She eyed Amelia then looked at John. Wordlessly she held out his gun.

John took it, clicked on the safety and slid it into the holster on his thigh. He looked at Amelia. "We need to get to the control room. I want a thorough check of all systems just to be sure she's operating properly."

"Yes, sir."

John watched her leave. He looked at Moira as she turned to him. He drew her into his arms. "You okay, baby? Fuck that was hot…my little gunslinger." He smiled.

"John!" She hit his chest. "Are we okay? I mean the city?"

"I don't know. Let's find out. I don't know about you but I could murder a burger about now."

"I…I can't...I mean I'll go get something now and eat in our room, okay? I can't face all of them, John, I can't so I'll be in my my my room," she stammered, sliding free of his embrace.

"Moira?" he asked, but she was gone, fleeing the room and fleeing him. He sighed, tempted to go after her. Instead he headed for the control room.

Everyone was there, talking at once, gesticulating wildly in the air but at his approach all the voices stopped and all eyes were on him. Wordlessly he moved to the monitors, checking each one, checking the system's output and the scans. Finally he met their gazes, expression stern.

"John?" Rodney asked to break the tension.

"So far so good. Do we have an ETA on when the shield will come down?

Rodney eyed the screen, relaxing. "About an hour, maybe two. The cloak will automatically engage, I've already set the protocols."

"Good. And the fuglies?"

"Fugly One is obliterated. Fugly Two is moving out of orbit, damaged," Jason answered. "Sir."

"Keep tracking that ship. I want to know where it goes and what it meets. And scan for any and all radio transmissions and all forms of communications. I want a real-time trajectory for that ship and any others out there."

"Yes, sir!"

"Wait…wait, they're going away, right? Obviously your plan worked and they think whatever was down here was destroyed. You…oh no."

"Oh no what?" Amelia asked, as Rodney was staring at John.

"He's going after them," Ronon informed, recognizing the resolve in John's eyes all too well. He smiled.

"What? Are you crazy?" Rodney exclaimed. "You said it yourself! We don't have the firepower to fight them, especially now!"

"I know…but we will," John said calmly.

"What? How? John, what the hell is wrong with you? We barely survived this!"

"I have to agree with Doctor McKay," Amelia stated, moving to stand next to the scientist. "We were almost toast back there! We don't have the weapons or the resources or the manpower to go up against one of those thinsg again, let alone a whole fleet of them!"

"Last I looked this wasn't a democracy, so there won't be a vote," John said curtly. "We're not going anywhere yet. We've got a little breathing room so I suggest we make the most of it. I need a hot dinner, a hot shower, and several hours of sleep."

Without another word he turned and left the control room.

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Moira whirled as the door to her room opened. She stared as John advanced. His gaze raked over her wet hair, the lilac nightshirt clinging to her curves. His gaze darted to the empty plate on the table, the empty glass next to it, then back to her. "Um, John?"

He stepped to her. He touched her arm. He pulled her into a lengthy kiss, shoving her body into his. "Moira," he breathed into her ear. He stepped back from her to take her hand. He eyed the bruises on her wrist, scowling.

"John?" she repeated, dazzled by the kiss. "I ate. I was, was just going to bed. Have you eaten? You need to eat something and then get some sleep, John. John, I'm fine…I'm fine…" she tried to pull free but his grip was strong, yet gentle.

He met her worried gaze. "Stop this, Moy."

"Stop what, John? You need to eat and then get some sleep. We're safe, right?"

"Yes, we are. You need to stop pulling away from me."

"I'm not! I just need to sleep! I just need to, to, to…." Her words failed as tears blurred her vision. "Please, John…"

Reluctantly he freed her wrist. "I'm going to get some dinner and then I'll be back, Moira. You are perfectly safe now, I promise. Do you need anything?"

"No. I'm fine. Go." She moved to the bed and got in under the blankets.

John watched her. He sighed. He turned and exited the room.

Moira almost called out after him but remained silent.


	6. Chapter 6

Stargate Atlantis: S7 The Fossil Key

Part Four: Trophic Cascade6

John let the hot water pound into him. He felt better after a hearty meal and a few beers. He had said little during the meal, letting the others talk and vent and celebrate. He wouldn't answer their inquiries into his plans, but he did smile when Rodney asked after Moira and Carson once again expressed his shame and horror at what he had done.

Now the hot water was driving all of that way, cascading along his body to soothe sore muscles and weary limbs. He closed his eyes, tilting his head back to seemingly drown in the downpour. Hearing a noise he opened his eyes, looking round. Steam filled the bathroom. Waves of mist rose all around him as he shut off the water.

Grabbing a towel he hastily wrapped it around himself and stepped out of the shower. "Moira?" He crossed the bathroom to peer into the bedroom. Shadows crisscrossed the room as the city lights played softly through the window. He could see her form in the bed. She was asleep. He rubbed his temples and returned to the bathroom to dry off and slide into his pajamas.

The steam was clearing and he glanced at the mirror to see his reflection slowly emerge; a dimly seen image of a long, lean man with disordered dark hair and scruff lining his jaw. There was a wavering image of a woman behind him.

John whirled. The bathroom was empty. His heart pounded. He turned back to see himself in the mirror. There was no one else there. He tried to relax, attributing the mirage to fatigue. He exited the bathroom and made his way to the bed. He slid in under the covers and next to Moira. He scooted close to her, spooning against her as she was on her side away from him. He slid his arm around her waist and closed his eyes, letting her warmth and the comfort of the bed lull him into a light doze.

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_She was riding him. She was riding him hard, bouncing up and down as the lights played across the curves of her back, her rear. Her hair flew all around her and her breasts were bouncing, her torso leaning as she took all of him into her. She was moaning softly, reaching the climax and he thrust up eagerly into her, over and over until he groaned and she cried out loudly._

_He looked over at the figure in the door and smiled, just smiled as Colonel Sheppard stood watching him fuck Moira._

Jason woke with a start. He sat up, sweating. He looked round the room, but he was alone. He reclined, wincing as the dream had given him a hard-on and it was almost painful. He smiled and reached down to relieve it, closing his eyes to resume the dream.

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_The ship was closing in fast. The vessel was enormous, twice the size of any Wraith cruiser and bristling with weaponry. The turrets were starting to open and to glow as the lasers charged, charged to fire at any second. He gripped the controls of the fighter, determined to find the exact spot to bring the enemy ship down. He had calculated the exact amount of energy needed and the dangerous combination of matter and anti-matter was his own invention; his own version of the Penning trap._

_He fired and the fugly ship exploded, but not before it dropped a bomb onto the heart of Atlantis that floated beneath it._

Rodney woke suddenly, grabbing at the blankets. He stared round, disturbed by the dream. He listened. The city was safe, secure and quiet in the middle of the night. No alarms blared to warn of any impending attack. He shook his head, settling back into the bed, relaxing as his mind worked over the idea of creating his own version of a Penning trap.

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_It was stalking the city. It was huge, ugly and a brute. It stalked the city, snarling with its red mouth and ugly teeth. The lights cast odd shadows along its gray skin and the neural implant was a red glare that blinked in time to his heartbeat. He watched it advance as it held its gun at its side, not fearing any opposition. It was too late. It didn't see the trap and walked right into it. Gunfire mowed it down, cut it to pieces but just to be sure he advanced and struck off the thing's head with one massive sweep of his sword._

_Only he had been the stupid one. It wasn't alone. They never traveled alone and he turned too late as the second one struck out with a weapon._

Ronon sat up so quickly he almost dislodged Amelia from the bed. He stared at the darkness, heart pounding as the dream faded. He tried to relax. There were no fuglies in Atlantis. The creatures had never even infiltrated the city; that had been Moira's hallucinations, not reality. He swallowed, reclined again and stared at the ceiling, knowing he wouldn't sleep the rest of the night. He plotted how best to kill one.

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_He stared at the blood on his hands. He had done his best, but he couldn't save everyone, not all of the time. He moved to the tray of instruments and began to methodically clean them. There was no one else to aid him so he did everything himself. He scrubbed at the scalpels, the knives and the electrodes, wiping them clean for the next time, except there wouldn't be a next time._

_She was cured. He looked over at the bed where his patient was locked in the restraints. There would be no more hallucinations. Moira was dead._

Carson cried out and bolted upright, fighting the blankets until he realized he was in bed, the victim of a terrible nightmare. He tried to calm himself, breathing heavily as his guilt berated him once more. He almost got up to go see Moira, to be sure she was all right, but he knew that she was secure in John's care. He reached over with a shaking hand and grabbed a bottle of pills. He downed two and settled into a dreamless sleep.

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_They were holding her down. They were all holding her down, forcing her to remain on the bed as the restraints were fastened one by one, so tightly even the padding cut into her flesh. They were all mocking her and laughing; they seemed almost jubilant at her distress and discomfort. They made sure she couldn't escape, couldn't move and she could hear the machine humming as it was charged with power. She could see the glint of a scalpel shining silver in the light. _

_Worst of all she as she struggled she could see John standing nearby, just standing and watching with an expression of boredom on his handsome face._

"No, no, NO!" Moira fought free, wildly. She woke John with an elbow to the ribs and a kick to his thigh. She scrambled out of the bed, falling hard onto her knees as the blankets trapped her and entangled her. She scurried out of them and lurched to her feet. The floor was cold but her skin was colder as shivers shot up and down her back.

"Whoa, whoa, Moy!" John leapt out of the bed and moved to her. "Sweetheart, it's all right."

"No! They were all holding me down! They were all complicit, John, all of them! Even you! You just stood there and did nothing, did nothing!" she accused, backing away from him.

John froze, staring at her. "It was a dream, Moira. If it had been real I would have done anything and everything to get you free. I would have killed anyone who got in my way."

"You…you just…you just stood there while they, they…" She touched her temple where a bruise purpled her skin.

John moved to her. "No, Moy. I would never let anyone hurt you. I'd die before that happened. It won't happen again, I promise. Moira." He caught her hand and ran his fingers gently over the bandage wrapping her wrist.

"I…it was so real, John. Sorry. I just…I don't know what's real and what's not real anymore. Parts of my my memory are missing but some things are clear."

"Like when Amelia held you down?" he asked. His voice was low, soothing. His gaze locked with hers.

"Yes. She, she thought she was helping. She didn't see what was in Carson, what…it's like the contagion spread, that it infected everyone in some way, trying to bend their minds, their will…the ATA gene carriers most of all because of the connection…"

"Yes, easier access, that makes sense, Moy," John mused.

"I can't."

"Can't what, Moira?"

She tugged free and held up her left hand. She began to pull off the gold ring. "I can't marry you. I can't. I love you, John, I love you but I can't marry you, okay?"

"What? No, it's not okay! You already answered, Moira. You said yes and you can't take it back now," he argued, not knowing whether to be amused or dismayed.

"I can't marry you, John! Can't we just leave things the way they are now? I can't marry you when I'm like this, when I don't know who to trust or believe and I won't put you through that, I just won't!"

"You can trust me, Moira, and I've been through it. You're stronger, Moira, and you can get through it, we both can."

"No! You're not listening! I can't…what the fuck did you do? Glue this on me?" she flared angrily, tugging and tugging but the ring wouldn't move past her knuckle.

John smirked. He caught her hand and pushed the ring back down. "If that's what it takes, yes, baby. You are going to marry me, Moira, and whatever shit is still going on we will handle it together, like always."

She stared at him a moment, furious, confused. "John!" She flung herself into his arms, kissing him. Kiss after kiss as his arms went around her and he returned her affection eagerly, hungrily now as his body began to respond to hers as it squirmed along his.

It was a matter of moments to gently push her against a wall. It took mere seconds to yank up her nightshirt and to free himself from his pajama pants. It took one second to thrust into her and he groaned with satisfaction as her moist tightness enfolded him and welcomed him. He thrust and thrust, hard and eager as he kissed her deeply, holding her gently to the wall and expending his emotions into her, onto her.

Moira squirmed, feet slipping and sliding as his kisses devoured her, as his cock plied her relentlessly. She whimpered and moaned into his mouth as the pleasure built and built to a crescendo of release. John shuddered, coming inside her. He freed her mouth to groan and to press himself against her. His hold tightened briefly then relaxed as she cried out with the tide of orgasm that melted her.

John kissed her, slid out of her and led her to the bed. He paused only to remove his pajamas, watching as she pulled off her nightshirt and scrambled under the blankets. He smiled. He yanked the blankets off her and slid over her, kissing her, aligning his body to hers. "Ah, baby…fuck that was hot. But now we can take our time. Moira?"

She kissed him, thighs opening in welcome. "Yes, John. John…oh sweetie, you what?"

John was staring at her. He lifted slightly and touched her wrist where bruise encircled it like a bracelet. He tenderly kissed the injured skin then ran his mouth up to her fingers. "I promise you, Moy…no one will ever hurt you again." His voice was low, raw and it made her shiver as it skimmed along her skin.

"Okay, John."

"You believe me?" he tested, oddly serious.

She touched his jaw. "Yes, John."

"Do you trust me?"

"Yes." She kissed him. "John? I, I didn't mean what I said earlier…I was upset by the nightmare and everything that's happened. John, are the Homo erectus really gone now?"

He seemed to relax. "Yes, Moira." He kissed her, shifting on her. "But this erectus is raring to go, baby."

Moira smiled.


End file.
